an indexing problem on postgreSQL

All,

I have an data-driven web application with Java and PostgreSQL. We have
a few tables which hold quite large amount of data. Therefore we put
indexing (B-tree) on them to make query faster. In addition, we are also
doing data synchronization on these tables with another microsoft FoxPro
application in real-time. Normally the indexing works just fine without
data synchronization. But with data synchronization, after a period of
time, the indexing did not take effect on the table so that the
application goes extremely slow.

Does anyone there has an idea why and have a solution to the problem?

Your help is greatly appreciated.

Sincerely,

-John